/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.utils.smithwaterman;

/**
 * Author: wbc
 */
public final class Parameters {
    public final int w_match;
    public final int w_mismatch;
    public final int w_open;
    public final int w_extend;

    /**
     * Create a new set of SW parameters
     * @param w_match the match score
     * @param w_mismatch the mismatch penalty
     * @param w_open the gap open penalty
     * @param w_extend the gap extension penalty

     */
    public Parameters(final int w_match, final int w_mismatch, final int w_open, final int w_extend) {
        if ( w_mismatch > 0 ) throw new IllegalArgumentException("w_mismatch must be <= 0 but got " + w_mismatch);
        if ( w_open> 0 ) throw new IllegalArgumentException("w_open must be <= 0 but got " + w_open);
        if ( w_extend> 0 ) throw new IllegalArgumentException("w_extend must be <= 0 but got " + w_extend);

        this.w_match = w_match;
        this.w_mismatch = w_mismatch;
        this.w_open = w_open;
        this.w_extend = w_extend;
    }
}
